Oropouche virus cases identified in Ecuador using an optimised qrt-pcr informed by metagenomic sequencing

Emma L. Wise, Sully Márquez, Jack Mellors, Verónica Paz, Barry Atkinson, Bernardo Gutierrez, Sonia Zapata, Josefina Coloma, Oliver G. Pybus, Simon K. Jackson, Gabriel Trueba, Gyorgy Fejer, Christopher H. Logue, Steven T. Pullan

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published qRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an qRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68–99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.

Original languageEnglish
Article numbere0007897
Pages (from-to)1-15
Number of pages15
JournalPLoS Neglected Tropical Diseases
Issue number1
StatePublished - Jan 2020


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